Additionally, the output from indexing and integrating is space group 16. The scaling is in space group 19

Dear Gabby,

if I recall correctly, SG 16 is P222 and SG 19 is P212121. So basically, what is happening is that the program is indexing and integrating in the Laue group primitive orthorhombic P222, but then, looking at systematic absences, it outputs space group P212121. Nothing wrong or cumbersome here.

If you want to process with XDS in lower symmetry, here's what you should change in your XDS.INP file:

SPACE_GROUP_NUMBER= 16 UNIT_CELL_CONSTANTS= a b c alpha delta gamma

Anyway, I take this opportunity to make a shameless advertisement (although I am not part of the team or have any interest in this advertisement whatsoever): try to process your data with autoPROC (https://www.globalphasing.com/autoproc/). autoPROC is a pipeline of programs that uses XDS, POINTLESS, AIMLESS and STARANISO for data reduction, space group assignment and iso/aniso scaling, respectively.

The program is quite visual and intuitive, and it will tell (you will see it!), what is happening with your data and what you can do to test different space groups or try different protocols to improve statistics.

Anyway, coming back to the beginning, if you are phasing by molecular replacement, you can use your P222-reduced dataset, and ask the MR program (usually PHASER), to try "all possible in same point group). This way you will know for sure if it's P222 or any of the subgroups of it.

Please contact me in private if you need further assistance.

Best regards,

Jose